rs11642603

chr16-30874900-C-Gchr16-30874900-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000572628.5(BCL7C):c.526+13960G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 152,258 control chromosomes in the GnomAD database, including 472 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.068 (472 hom., cov: 31)
• Consequence: BCL7C ENST00000572628.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

Genes affected

BCL7C (HGNC:1006): (BAF chromatin remodeling complex subunit BCL7C) This gene is identified by the similarity of its product to the N-terminal region of BCL7A protein. The BCL7A protein is encoded by the gene known to be directly involved in a three-way gene translocation in a Burkitt lymphoma cell line. The function of this gene has not yet been determined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCL7C	NM_001286526.2	c.528+13960G>C		intron_variant
BCL7C	XM_011545980.4	c.528+13960G>C		intron_variant
BCL7C	XM_047434896.1	c.621+5324G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL7C	ENST00000380317.8	c.528+13960G>C		intron_variant		1		A1
BCL7C	ENST00000572628.5	c.526+13960G>C		intron_variant		1
BCL7C	ENST00000574418.5	c.*71+13960G>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 10369 AN: 152140 Hom.: 472 Cov.: 31

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0555

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0347

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0664

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0681 AC: 10364 AN: 152258 Hom.: 472 Cov.: 31 AF XY: 0.0654 AC XY: 4867 AN XY: 74452

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.0554

Gnomad4 ASJ AF: 0.0646

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0568

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0657

Alfa AF: 0.0402 Hom.: 33

Bravo AF: 0.0664

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.0
Dann	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11642603; hg19: chr16-30886221;